1b.Approach (from AD-416)
Develop and release improved apple rootstocks. Perform all breeding and evaluation stages involved in the 15-25 year process of developing new rootstocks with the assistance of recently developed breeding tools, such as marker-assisted selection. Develop improved propagation methods that speed the distribution of selected material to customers through established networks of cooperating nurseries. Exogenous treatments of layering propagation stool beds will increase adventitious root formation and quality of nursery liners. Incorporate innovative concepts of orchard establishment and management including mechanization. Existing experimental rootstocks in the breeding pipeline possess adaptations for novel orchard concepts and mechanization. Develop and apply genomic and bioinformatic tools to marker-assisted selection of apple rootstocks. Develop algorithms to assist with identifying specific markers for priority horticultural traits from the large body of expressed sequence tags (EST) and genomic sequence data now available.

3.Progress Report
We placed into tissue culture several new improved apple rootstocks nearing release phase. This step is critical to increase the number of plants tested and available before full release to the industry. We coordinated efforts by six U.S. apple rootstock nurseries to tissue culture, micropropagate and conduct research on improving propagation properties of G.41, G.935, G.11, and G.202. This year we should have over 300,000 rootstock plants available for the establishment of new stool propagation beds. We started an effort to compare performance of apple rootstocks derived from tissue culture to conventional propagation. Every year we harvest apples (count and weigh) from trees grafted onto our experimental rootstocks to select the ones that yield early and heavy. We have made 24 selections this year. Every year we also harvest apple rootstock liners from small propagation beds. In FY08 we harvested, evaluated and characterized over 3,000 of these liners for their propagation properties. Every year we use selected apple rootstock liners to make (graft) test trees in our ‘in house’ nursery, in FY08 we planted about 2,500 liners to be made into new trees and a portion of harvested liners were shared with our cooperating nurseries and researchers. Among recipients were Dr. David Bedford for advanced testing with new scion varieties in the University of Minnesota; Dr Renae Moran University of Maine to test cold hardiness of G.41. This year we harvested about 3,500 finished trees and planted a new orchard aimed at evaluating tree architecture properties of rootstocks. In collaboration with Dr. Aldwickle we completed characterization of fire blight resistance (two strains) in elite germplasm near release revealing weak resistance to the aggressive strain in three rootstocks. With Drs. Aldwinckle and Norelli (ARS, Kearneysville) we identified genes active in fireblight response in apple.
We continued a major effort into diagnostic DNA fingerprinting of apple rootstocks for proper identification of misidentified rootstocks and avoidance of potential downstream planting and propagation problems. We have utilized the apple rootstock genetic map produced in house in conjunction with phenotypic data for fire blight resistance, spine production (a nursery trait), powdery mildew resistance, dwarfing, and root architecture to discover the genic regions that modulate these traits. We detected while phenotyping roots in the mapping population three QTLs for production of fine roots. This feature may be connected to the excellent results with replant disease resistance collected on the project on Apple Replant Disease Tolerance Evaluation in collaboration with Tom Auvil and Dr. J. McFerson of the Washington State Tree Fruit Research Commission and ARS scientist Dr. Mazzola of the Wenatchee ARS location. We have continued to work on genomics of apple scion gene expression modified by diverse apple rootstocks in collaboration with Dr. McNellis and Dr. Jensen (PSU). We also made good progress on Graft Transmissible Gene Silencing of Apple Scion Genes from Transgenic Apple Rootstocks in collaboration with Dr. Norelli (ARS, Kearneysville). 301 Comp. 2a,b, 1c.

4.Accomplishments
1.
Characterization of nursery tree scion architecture modification by apple rootstocks
One of the problems that finished tree nurseries and apple growers face is choosing a rootstock that has the ability to generate a good quality tree that yields high early production. Finished tree quality for an apple tree is usually defined by tree caliper but the number of feathers and the angle of the feathers are also important criteria in evaluating tree quality. We have observed that many of the Geneva rootstocks have flatter branches and more feathers than similar commercial rootstocks. This is a significant advantage in high density systems such as the Tall Spindle since less labor would be required to tie feathers or branches down after planting. This trait is useful when pairing rootstocks with upright growth-habit scion varieties to decrease vigor and increase productivity. To measure the rootstock effect on branch angles and number of feathers we set up a replicated trial (randomized complete block) at a commercial nursery site (Willow Drive, Ephrata, WA) by grafting the same scion (Brookfield Gala) onto 25 different commercial and experimental rootstocks belonging to dwarfing classes 2-7. We measured rootstock and tree quality attributes including rootstock liner caliper and canopy, tree caliper, tree height, number of branches (feathers) per tree, branch origination height, branch angle and branch length. There are two major impacts that this study has accomplished: 1. We now know that we can utilize rootstocks to change the architecture of the orchard which may lead to ways to mechanize pruning. 2. Growers and nurseries can utilize this knowledge to pair specific scions with these rootstocks to obtain better tree quality and orchard architecture.
This accomplishment relates to National Program 301 (Plant, Microbial, and Insect Genetic Resources, Genomics, and Genetic Improvement) Action Plan Component 2b, (Genetic Improvement).

2.
Discovery of genic regions affecting several critical apple rootstock traits
One of the major problems that we face in apple rootstock breeding is the long evaluation time needed to select individuals for a positive apple rootstock trait. We found the location of gene regions that control important apple rootstock traits. We connected data on fire blight resistance, powdery mildew resistance and root architecture to regions of the apple genome exemplifiend in a genetic map that we developed in the previous year (Ottawa 3 X Robusta 5 genetic map) to discover four regions modulating fire blight resistance, three regions that modulate powdery mildew resistance, four regions associated with number of internodes produced each season (a component of dwarfing) and three regions that modulate fine root formation – a trait that may be connected to replant disease tolerance. We are utilizing the knowledge about the location and complexity of these traits to streamline our breeding program through the implementation of Marker Assisted Breeding – which will be particularly important for traits that are difficult to evaluate (e.g. root morphology) or that take a long period of time to develop (e.g. dwarfing). This accomplishment impacts the ability of the breeding program to select positive traits early before they are planted in the field, thus increasing the efficiency of the breeding program. This study also impacts the way we look at replant disease resistance – where root architecture features may have an effect on this important trait. This accomplishments relates to National Program 301 (Plant, Microbial, and Insect Genetic Resources, Genomics, and Genetic Improvement) Action Plan Component 1c (Documentation and Characterization of Genetic Resources), Action Plan Component 2a (Genome Characterization), and Action Plan Component 2b, (Genetic Improvement), and to National Program 303 (Plant Disease) Action Plan Component 5 (Host Plant Resistance to Disease).